Java (JAR)
Installing Java JAR
Installing Java JAR
Google the package: GATK
In this case: need to create an account with the Broad institute
Download the GATK 3.6 to your computer
Upload the zipped file to your /home directory on the cluster
Unzip the files on your home directory: /home/XXX/gatk
Create the necessary environment variable (see Module section), .e.g. export GATK="/home/XXX/gatk/GenomeAnalysisTK.jar
Run your binaries on the cluster
java -jar /home/XXX/gatk/GenomeAnalysisTK.jar -h
java -jar $GATK -h (optional - if this is setup in .bashrc file)
java -jar /home/XXX/gatk/GenomeAnalysisTK.jar -T CountReads -R exampleFASTA.fasta -I exampleBAM.bam